Contacts of the strand formed by residues 218 - 225 (chain 1) in PDB entry 1SVA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 218 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1531 ALA* 4.1 3.5 - - - +
1541 VAL 3.5 9.6 + - - -
1551 GLY* 3.4 16.6 - - - -
1571 GLU* 4.1 9.4 - - + +
1581 PRO 3.9 18.4 - - - +
1591 LEU* 3.9 17.3 - - - +
1601 GLU* 5.2 1.8 - - - +
2151 ASN* 3.2 32.6 + - + +
2171 ASN* 1.3 81.6 - - + +
2191 ARG* 1.3 89.9 + - - +
2201 TYR* 5.4 0.2 - - - -
2521 PRO* 4.4 1.1 - - - -
2385 ASN* 3.2 17.5 + - - -
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Residues in contact with ARG 219 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1531 ALA* 2.8 25.6 - - - -
1541 VAL 2.9 15.8 + - - +
2151 ASN 4.8 0.4 + - - -
2161 GLU 3.6 19.8 + - - -
2171 ASN* 4.4 2.4 + - - +
2181 THR* 1.3 97.8 + - - +
2201 TYR* 1.3 62.7 + - - +
2211 PHE* 3.6 23.7 - - + -
2441 LEU* 2.7 39.3 + - + +
2451 LEU 4.2 3.4 + - - -
2461 ASP* 3.2 18.4 - - - +
2501 VAL* 2.9 28.7 + - - +
2511 GLY* 3.6 8.5 - - - -
2521 PRO* 4.2 8.2 - - + +
2385 ASN* 3.6 11.5 - - - +
2395 THR* 4.1 18.8 - - + +
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Residues in contact with TYR 220 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1511 PHE* 3.2 21.8 - + + -
1521 PHE 3.3 4.7 - - - -
1531 ALA* 3.7 6.1 - - + -
1591 LEU* 5.0 2.5 - - + -
2101 PRO* 3.5 31.0 - - + -
2121 PRO* 3.7 18.8 - - + +
2151 ASN* 4.6 15.0 - - + -
2181 THR* 5.4 0.2 - - - -
2191 ARG* 1.3 77.1 - - - +
2211 PHE* 1.3 76.8 + - - +
1185 GLU* 2.7 28.1 + - - -
2365 ILE* 3.5 12.8 - - + -
2375 THR* 3.2 35.8 + - - +
2385 ASN* 2.9 63.1 + - + +
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Residues in contact with PHE 221 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1511 PHE* 3.0 6.7 - - - -
1521 PHE* 2.8 74.4 + + + -
2191 ARG* 3.6 36.8 - - + -
2201 TYR* 1.3 83.9 - - - +
2221 GLY* 1.3 59.2 + - - +
2421 THR* 4.3 22.2 - - + -
2431 VAL 4.9 3.1 - - - -
2441 LEU* 4.7 8.3 - - + -
2365 ILE* 3.7 1.3 - - - -
2375 THR* 3.5 13.0 - - + +
2395 THR* 3.5 28.9 - - + -
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Residues in contact with GLY 222 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491 PHE* 4.4 1.1 - - - -
1501 HIS 3.1 13.5 - - - -
1511 PHE* 3.8 5.8 - - - -
2211 PHE* 1.3 76.6 - - - +
2231 THR* 1.3 70.9 + - - +
2355 HIS* 3.1 3.1 - - - +
2365 ILE* 2.8 44.1 + - - +
2375 THR* 4.0 1.0 + - - -
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Residues in contact with THR 223 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1481 ASN* 4.4 0.9 - - - +
1491 PHE* 3.6 22.1 - - - -
1501 HIS* 3.1 16.1 + - + +
2221 GLY* 1.3 83.5 - - - +
2241 TYR* 1.3 63.1 + - - +
2251 THR* 3.7 12.0 + - - -
2335 VAL* 5.4 2.2 - - - +
2345 LEU 2.9 7.0 - - - -
2355 HIS* 3.3 36.0 + - + +
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Residues in contact with TYR 224 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471 SER* 3.6 12.9 + - - -
1481 ASN 3.8 9.6 - - - -
1491 PHE* 3.6 19.9 - + + -
2231 THR* 1.3 74.9 - - - +
2251 THR* 1.3 63.3 + - - +
2261 GLY* 3.1 35.2 - - - -
1225 VAL* 3.0 41.7 - - + +
1255 MET* 3.5 48.7 + - + +
1265 LEU* 3.9 29.8 - - + -
1435 PRO* 4.6 3.6 - - - +
2325 PRO* 4.1 3.8 - - + -
2335 VAL* 3.3 4.9 - - - +
2345 LEU* 2.7 42.1 + - + +
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Residues in contact with THR 225 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471 SER* 3.5 3.8 - - - -
1481 ASN* 3.0 49.6 + - - +
2231 THR* 3.7 11.4 + - - -
2241 TYR* 1.3 79.8 + - - +
2261 GLY* 1.3 62.5 + - - +
2301 VAL* 4.1 22.7 - - + +
2311 PRO 5.8 1.3 - - - +
2315 PRO* 5.3 2.0 - - + -
2325 PRO 3.4 9.9 - - - +
2335 VAL* 4.2 16.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il